MolNFT v1 · #155456 · protein + DNA

Complex of DNA polymerase IV and D-DNA duplex

6L84: “Complex of DNA polymerase IV and D-DNA duplex”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.78). MolNFT v1 #155456 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6L84
Type: protein + DNA
Length: 370 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA polymerase IV; DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3'); DNA…
EC: 2.7.7.7
UniProt: Q97W02
Ligands: CA
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	341	44% helix, 25% strand	Q97W02
P	DNA (5'-D(GPGPGPGPGPAPAPGPGPAPTPTPCPC)-3')	dna	14	—	—
T	DNA (5'-D(PCPGPGPAPAPTPCPCPTPTPCPCPCPCP*C)- 3')	dna	15	—	—

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, P

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	783	0.78	0.82	53	empty
2	384	0.72	0.84	44	empty
3	315	0.59	0.78	38	CA
4	91	0.44	0.80	15	empty

Interfaces

3 interfaces between chains.

A–T · 960 Å² buried · 23 hydrogen bonds · protein-nucleic
A–P · 733 Å² buried · 16 hydrogen bonds · protein-nucleic
P–T · 606 Å² buried · 57 hydrogen bonds · nucleic-nucleic

Compared structures

6L84 · Complex of DNA polymerase IV and D-DNA duplex · the same entry in another collection · chain A against A, TM-score 1.00
Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q97W02
Elsewhere: RCSB PDB 6L84 · PDBe 6L84 · UniProt Q97W02

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